Noi/NOTES/2012-3-24: Difference between revisions
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== Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]] == | == Link to calendar: [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes]] == | ||
=== ASM analysis of UCLA SZ data set === | |||
* Continued from 2012_03_24: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23]] | * Continued from 2012_03_24: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-23]] | ||
* Plotting the distance between SNP-CpG showing ASM and -log10(p-value) | |||
awk '{print $1"\t"$98}' UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt | sed s'/:/\t/g' | awk '{print $2-$3"\t"$98}' > UCLA_SZ_SeqDep_TTest-noSNP-SNP-CpG_distance_PVal0.05.txt | |||
Note: In UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt file, $2 = SNP position, $3 = CpG position, and $98 = p-value from T-test | |||
* In excel taking -log(p-value) and plot graph either absolute distance or distance between SNP-CpG | |||
[[File:SNP-CpG_distance-logp-val.png| 500px]] [[File:absSNP-CpG_distance-logp-val.png| 500px]] | |||
* Useful link for Ven diagram by R: http://www.ats.ucla.edu/stat/r/faq/venn.htm | * Useful link for Ven diagram by R: http://www.ats.ucla.edu/stat/r/faq/venn.htm |
Revision as of 00:08, 25 March 2012
Link to calendar: [[1]]
ASM analysis of UCLA SZ data set
- Continued from 2012_03_24: [[2]]
- Plotting the distance between SNP-CpG showing ASM and -log10(p-value)
awk '{print $1"\t"$98}' UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt | sed s'/:/\t/g' | awk '{print $2-$3"\t"$98}' > UCLA_SZ_SeqDep_TTest-noSNP-SNP-CpG_distance_PVal0.05.txt Note: In UCLA_SZ_SeqDep_TTest-noSNP_PVal0.05.txt file, $2 = SNP position, $3 = CpG position, and $98 = p-value from T-test
- In excel taking -log(p-value) and plot graph either absolute distance or distance between SNP-CpG
File:SNP-CpG distance-logp-val.png File:AbsSNP-CpG distance-logp-val.png
- Useful link for Ven diagram by R: http://www.ats.ucla.edu/stat/r/faq/venn.htm